fixed intercept parameter name when using geom_vline

chipseq_workflow/cs_region_dba.R

@@ -81,12 +81,12 @@ deResults %>% with(as.data.frame(table(sample_1, sample_2)))
 #+ fig.width=20, fig.height=18
 deResults %>% ggplot(aes(log2FoldChange)) +
     geom_histogram(binwidth=0.1) +
-    facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0, color="blue") +
+    facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0, color="blue") +
     xlim(-4,4)
 
 deResults %>% ggplot(aes(pvalue)) +
     geom_histogram() +
-    facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue")
+    facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue")
 
 ### see https://www.biostars.org/p/80448/ for Pairwise Comparison
 #res <- results(dds, contrast=c(c("condition","H1M_Dome","H1M_Shield")))

chipseq_workflow/peak_report.R

@@ -61,7 +61,7 @@ peaks %>%
     ggplot(aes(peak_width)) +
         geom_histogram() +
         facet_grid(sample ~ peak_type)  +
-        # + geom_vline(yintercept=0, color="blue")
+        # + geom_vline(xintercept=0, color="blue")
         ggtitle("peak width distribution") +
         xlim(0,1000)
 
@@ -71,7 +71,7 @@ peaks %>%
         geom_jitter(alpha=0.05, data=sample_frac(peaks, 0.1)) +
         geom_violin(alpha=0.8) +
         facet_wrap(~ peak_type)  +
-        # + geom_vline(yintercept=0, color="blue")
+        # + geom_vline(xintercept=0, color="blue")
         ggtitle("peak width distribution") +
         ylim(0,1000)
 
@@ -82,7 +82,7 @@ peaks %>%
         geom_jitter(alpha=0.05, data=sample_frac(peaks, 0.1)) +
         geom_violin(alpha=0.8) +
         facet_wrap(~ peak_type)  +
-        # + geom_vline(yintercept=0, color="blue")
+        # + geom_vline(xintercept=0, color="blue")
         ggtitle("peak score distribution") +
         ylim(0,100) +
         rot_x_lab()

dge_workflow/dge_star_template.sh

@@ -135,8 +135,8 @@ rend.R -e $NGS_TOOLS/common/cp_enrichment.R --overlay_expr_data ../plot_score_ma
 
 ## bidirectional sync with project space
 ## todo define mount path on bioinfo for bidirectional synching
-~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
+## ~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
 
-# uni-directional sync
+# or use a uni-directional sync
 #rsync -avsn --delete  $baseDir brandl@fileserver:/projects//file/server/path
 mailme "$project: sync done"
\ No newline at end of file

dge_workflow/featcounts_deseq.R

@@ -225,7 +225,7 @@ deResults <- adply(contrasts, 1,  splat(function(sample_1, sample_2){
 
 deResults %>% ggplot(aes(s1_over_s2_logfc)) +
     geom_histogram(binwidth=0.1) +
-    facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0, color="blue") +
+    facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0, color="blue") +
     xlim(-2,2) + 
     ggtitle("sample1 over sampl2 logFC ")
 
@@ -236,13 +236,13 @@ deResults %>% ggplot(aes(s1_over_s2_logfc)) +
 #deResults %>% ggplot(aes(pvalue)) +
 #    geom_histogram() +
 #    xlim(0,1) +
-#    facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue") +
+#    facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue") +
 #    ggtitle("p-value distributions") #+ scale_x_log10()
 #
 #deResults %>% ggplot(aes(padj)) +
 #    geom_histogram() +
 ##    xlim(0,1) +
-#    facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue") +
+#    facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue") +
 #    ggtitle("Adjusted p-value distributions") #+ scale_x_log10()